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      Active Efflux Leads to Heterogeneous Dissipation of Proton Motive Force by Protonophores in Bacteria

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          ABSTRACT

          Various toxic compounds disrupt bacterial physiology. While bacteria harbor defense mechanisms to mitigate the toxicity, these mechanisms are often coupled to the physiological state of the cells and become ineffective when the physiology is severely disrupted. Here, we characterized such feedback by exposing Escherichia coli to protonophores. Protonophores dissipate the proton motive force (PMF), a fundamental force that drives physiological functions. We found that E. coli cells responded to protonophores heterogeneously, resulting in bimodal distributions of cell growth, substrate transport, and motility. Furthermore, we showed that this heterogeneous response required active efflux systems. The analysis of underlying interactions indicated the heterogeneous response results from efflux-mediated positive feedback between PMF and protonophores’ action. Our studies have broad implications for bacterial adaptation to stress, including antibiotics.

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          One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

          We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.
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            Bacterial persistence as a phenotypic switch.

            A fraction of a genetically homogeneous microbial population may survive exposure to stress such as antibiotic treatment. Unlike resistant mutants, cells regrown from such persistent bacteria remain sensitive to the antibiotic. We investigated the persistence of single cells of Escherichia coli with the use of microfluidic devices. Persistence was linked to preexisting heterogeneity in bacterial populations because phenotypic switching occurred between normally growing cells and persister cells having reduced growth rates. Quantitative measurements led to a simple mathematical description of the persistence switch. Inherent heterogeneity of bacterial populations may be important in adaptation to fluctuating environments and in the persistence of bacterial infections.
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              Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

              We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection'—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
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                Author and article information

                Contributors
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                13 July 2021
                Jul-Aug 2021
                13 July 2021
                : 12
                : 4
                : e00676-21
                Affiliations
                [a ] Department of Physics, Emory University, Atlanta, Georgia, USA
                [b ] Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
                [c ] Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
                University of Pittsburgh
                Author notes
                [*]

                Present address: Ekaterina Krasnopeeva, Institute of Science and Technology Austria, Klosterneuburg, Austria.

                Ekaterina Krasnopeeva and Faris Sinjab contributed equally to this work. Author order was determined both alphabetically and in order of increasing seniority.

                Author information
                https://orcid.org/0000-0003-1594-4971
                Article
                mBio00676-21
                10.1128/mBio.00676-21
                8406135
                34253054
                7053e5d1-9f6d-4fc2-af12-8420007ebe65
                Copyright © 2021 Le et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 8 March 2021
                : 4 June 2021
                Page count
                supplementary-material: 7, Figures: 4, Tables: 0, Equations: 0, References: 82, Pages: 9, Words: 6884
                Categories
                Research Article
                Custom metadata
                July/August 2021

                Life sciences
                bacterial physiology,single-cell microscopy,cell-to-cell heterogeneity,efflux pumps,proton motive force,protonophore

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